I have recently started to use bowtie2 with my de novo assembled reference.
I first repeat-masked my reference and executed bowtie2-build. Bowtie2 said 'Warning: Encountered reference sequence with only gaps' several times because some contigs were masked entirely.
I then mapped my fastq reads to the reference with bowtie2. Bowtie2 seemed to work fine but subsequent analysis, specifically GATK RealignerTargetCreator, failed with error message as below.
ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
I checked bam header.
$ samtools view -H bowtie2out.bam | grep 'scaffold299259_cov28'
@SQ SN:scaffold299259_cov28 LN:942
and the length of scaffold299259_cov28 in the reference fasta was indeed 314bp.
I am not sure but below might be cause.
The next two sequence of the scaffold299259_cov28 have been entirely masked by 'N' and summed length of three sequence (scaffold299259_cov28, scaffold317285_cov51 and scaffold333069_cov57) is 942. So, bowtie2-build might skip scaffold317285_cov51 and scaffold333069_cov57 headers.
Hi,
I have recently started to use bowtie2 with my de novo assembled reference.
I first repeat-masked my reference and executed bowtie2-build. Bowtie2 said 'Warning: Encountered reference sequence with only gaps' several times because some contigs were masked entirely.
I then mapped my fastq reads to the reference with bowtie2. Bowtie2 seemed to work fine but subsequent analysis, specifically GATK RealignerTargetCreator, failed with error message as below.
ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = scaffold299259_cov28 / 942
ERROR contig reference = scaffold299259_cov28 / 314.
I checked bam header.
$ samtools view -H bowtie2out.bam | grep 'scaffold299259_cov28'
@SQ SN:scaffold299259_cov28 LN:942
and the length of scaffold299259_cov28 in the reference fasta was indeed 314bp.
I am not sure but below might be cause.
The next two sequence of the scaffold299259_cov28 have been entirely masked by 'N' and summed length of three sequence (scaffold299259_cov28, scaffold317285_cov51 and scaffold333069_cov57) is 942. So, bowtie2-build might skip scaffold317285_cov51 and scaffold333069_cov57 headers.
If anyone knows solution for this matter, please let me know.
I really appreciate all of your helps.
best,
Takashi